Flight Commander

If a squadron activated by Yavaris moves during that ship’s activation, it loses the chance to resolve Yavaris‘ card effect.

For example, a ship equipped with Yavaris, Flight Commander, and Fighter Coordination Team cannot use Fighter Coordination Team to move squadrons, resolve a squadron command after executing its maneuver with Flight Commander, and then use Yavaris‘ effect to add an extra die to their attacks.

Reference

When a ship equipped with Flight Commander activates, after revealing the ships command dial, if you declare the resolution of Squadron Command, you may resolve Flight Commander’s ability to delay that resolution until after the ship executes a maneuver.

In regards to timing of declaring intent with Flight Commander and squadron command. A Squadron Dial or Token must be spent after revealing a ships command dial in order for Flight Commander to be resolved.

A player could not, for example, resolve Flight Commander attack with the ship, move the ship, and then token the squadron dial. As Dials can only be tokenized when they are revealed.

The controlling player decides when to fulfill Flight Commander’s ability if a ship was to conduct multiple maneuvers due to an ability such as Engine Techs or Rift Ambush objective special rule.